Probe-GridMap-Builder

🧪 Probe GridMap Builder

Probe GridMap Builder is a local web-based software interface designed to analyze molecular dynamics (MD) trajectories in .trr or .nc format, powered by the AMBER cpptraj backend. It enables users to generate grid-based interaction maps between protein structures and solvent probe atoms across dynamic frames. You can use this tool for free by clicking here. 👉 Live Demo

✅ Features

Upload .trr or .nc trajectory files
Grid map generation via cpptraj
Cluster analysis and PDB annotation via cluster.py
Automatic packaging of results (PDB + summary)

📦 Conda Environment Setup

# 1. Extract GridMap_denv.tar.gz 
tar -xzf GridMap_env.tar.gz

# 2. Activate Environment
source GridMap_env/bin/activate

🚀 Run the Server

python probe-gridmap.py

open the http://127.0.0.1:8082

📝 Usage

Upload your .trr or .nc trajectory file via the web interface.
Upload the corresponding .pdb file and choose probe atoms.
Submit the job, and download the result ZIP containing: • nonortho.pdb • nonortho_mark.pdb • cluster_summary.txt